Diversity and genetic structure within a Mexican maize race reveal consistent biocultural processes across geographic scales.

Abstract

Understanding how genetic diversity is distributed within maize races is critical for conserving maize genetic diversity. While maize races are traditionally treated as homogeneous units to be targeted by conservation, each race may encompass genetically distinct populations of landraces, shaped by environmental conditions and farmer selection. In this study, the genetic diversity and population structure of the Olotillo race were examined using 89,810 SNPs from 158 samples collected across local, regional, and national scales in Mexico. Additional samples from other races Dzit-bacal, Tuxpeno, and a Mix, group combining Olotillo with other varieties, brought the total to 171 individuals. Population structure analyses (ADMIXTURE, PCA) revealed that genetic clusters do not align with race identity, but instead reflect geographic origin. Inbreeding depression was evident within Olotillo populations, with mean FIS = 0.746 {+/-} 0.066. A heterozygote deficiency was observed: mean HeOB = 0.075 {+/-} 0.020, compared to a higher expected heterozygosity (HeEX = 0.295 {+/-} 0.002). Expected homozygosity (HOEX) of 0.705{+/-} 0.002 was observed, reflecting reduced effective genetic variation. The above is reflected in the population contraction signal (e.g., positive Tajimas D), and no significant differences between scales in HeEX, HOEX, and nucleotide diversity ({pi}), suggesting that similar evolutionary forces act across regions with a strong directional selection. These findings underscore the need to ascertain the genetic background among races and to recognize meaningful within-race differentiation. Conservation actions should reflect this structure, promoting targeted seed exchange to counteract genetic erosion while respecting farmer preferences. Olotillo exemplifies how maize diversity is structured not only by genetics, but by cultural and management systems that shape evolution in situ.